We further investigated whether adding African American samples to the discovery dataset can improve the prediction in the AFR population. Among the 33 traits we examined, 14 traits were also available in PAGE31 (N=11,178–49,796), a genetic epidemiology study comprising largely African American and Hispanic/Latino samples (Supplementary Table 10). All UKBB-PAGE and BBJ-PAGE genetic-effect correlations were moderate to high (range 0.44–1.00; Supplementary Table 10). Although the discovery and target samples had largely matched ancestry, applying PRS-CS (or other single-discovery methods) to PAGE summary statistics alone produced low prediction accuracy in the AFR population with only a few exceptions, due to the small sample size of the PAGE study (Fig. 3c; Supplementary Table 14). However, integrating UKBB, BBJ and PAGE summary statistics using PRS-CSx (Supplementary Table 15) dramatically outperformed single-discovery methods, and the median relative improvement in R2 was 28.1% when compared with PRS-CSx trained on UKBB and BBJ GWAS only, suggesting that PRS-CSx benefits from including samples that have matched ancestry with the target population in the discovery dataset, even if the non-European GWAS included are considerably smaller than European studies
